For thousands of years before the first rice paddies were carved into the landscape, the Jomon people thrived across the Japanese archipelago. These indigenous hunter-gatherer-fishers built a remarkably stable, deeply rooted island culture, leaving behind a rich archaeological record famous for some of the world’s earliest pottery (Cooke et al. 2021).
But from a genetic standpoint, the Jomon are an anomaly. They aren’t just “ancient Japanese” in a modern sense. Instead, modern mainland Japanese ancestry is a tripartite (three-part) cocktail (Okada et al. 2024).:
~12.4% Jomon (the original foragers)
~21.2% Northeast Asian (associated with the influx of Yayoi period farmers)
~66.4% East Asian (linked to Kofun period state formation)
Because of this distinct genetic layering, Japan serves as a fascinating evolutionary test case. If the ancient Jomon possessed a unique polygenic score (PGS) profile—the collective genetic variants that influence complex traits—does a shadow of that profile still linger in modern Japanese populations today?
To find out, I looked at three specific polygenic scores: educational attainment (EA), standing height, and a light-skin pigmentation score based on an East Asian GWAS (Kim et al., 2024).
The Ancient Baseline: How the Jomon Stood Out
To set the baseline, I pulled imputed ancient DNA from a broad East Asian dataset, grouping 17 ancient samples explicitly identified as Jomon. I then stacked them up against other ancient East Asian populations.
Because these ancient samples span a wide range of eras, a raw comparison could easily mask or mimic evolutionary shifts. To fix this, I adjusted the model for sample age. The numbers below reflect the standardized PGS effects driven strictly by Jomon group identity, independent of time.
Table 1. Time-adjusted Jomon PGS effects in the ancient dataset.
The Jomon are low for EA, extremely low for height, and high for the Kim light-skin score.
Figure 1. Time-adjusted ancient Jomon PGS compared with other metadata population groups.
The ancient Jomon pattern is clear: low EA, very low height, and high light-skin PGS. But the more interesting question is whether any of this survives in modern Japanese, who are mostly descended from later mainland-derived Yayoi and Kofun ancestry. That is where the result gets more complicated.